Is DPH1 p.Gln12Lys (c.34C>A) pathogenic?

DPH1 p.Gln12Lys (c.34C>A) is classified Uncertain significance in DPH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-05). AlphaMissense: likely benign (0.07); Absent from gnomAD v4.1; Associated with developmental delay with short stature, dysmorphic facial features, and sparse hair.

How common is DPH1 p.Gln12Lys (c.34C>A) in the general population?

DPH1 p.Gln12Lys (c.34C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DPH1 p.Gln12Lys (c.34C>A)?

AlphaMissense predicts likely benign (score 0.07) — an in-silico prediction, not a clinical call.

DPH1 p.Gln12Lys

Q: What condition is associated with DPH1 p.Gln12Lys (c.34C>A)?

DPH1 p.Gln12Lys (c.34C>A) is associated with developmental delay with short stature, dysmorphic facial features, and sparse hair (ClinVar).

c.34C>A · rs1285486074 · VCV1029332

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.07 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,599,800)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

developmental delay with short stature, dysmorphic facial features, and sparse hair

Computational evidence

Protein change
AlphaMissense	0.07	likely benign
REVEL	0.04	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.04	GERP 0.41, phastCons 0.002
Regional constraint	o/e 1.07	unconstrained · MANE · 12 kb · p 0.074 · regional, not allelic
Overall
CADD	9.101	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM Q17K vs ClinVar Q12K) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,599,800). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DPH1
Protein: p.Gln12Lys
Coding: c.34C>A
MANE Select: NM_001383
dbSNP: rs1285486074
Type: single nucleotide variant
Location: chr17:2030203 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.00
Residue 12: the 'disordered' region

Full DPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental delay with short stature, dysmorphic facial features, and sparse hair — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPH1 p.Gln12Arg Uncertain significance ★ ⚠ same residue
DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same condition
DPH1 p.Arg27His Uncertain significance ★★ ⚠ same condition
DPH1 p.Ile241Phe Uncertain significance ★★ same condition
DPH1 c.1228-21A>G Benign ★★ same condition
DPH1 c.400+117G>A Benign ★★ same condition
DPH1 p.Pro332= Benign ★★ same condition
DPH1 p.Tyr128His Likely pathogenic ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dph1-p-gln12lys (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown